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Phylogenetic relationships of xenodermid snakes (Squamata: Serpentes: Xenodermidae), with the description of a new genus
expand article infoV. Deepak§, Samuel Lalronunga|, Esther Lalhmingliani|, Abhijit Das, Surya Narayanan#, Indraneil Das¤, David J. Gower§
‡ Senckenberg Dresden, Dresden, Germany
§ The Natural History Museum, London, United Kingdom
| Mizoram University, Aizawl, India
¶ Wildlife Institute of India, Uttarakhand, India
# Ashoka Trust for Research in Ecology and the Environment, Bangalore, India
¤ Universiti Malaysia, Sarawak, Malaysia
Open Access

Abstract

Xenodermidae is a generally poorly known lineage of caenophidian snakes found in South, East and Southeast Asia. We report molecular phylogenetic analyses for a multilocus data set comprising all five currently recognised genera and including new mitochondrial and nuclear gene sequence data for the recently described Stoliczkia vanhnuailianai. Our phylogenetic results provide very strong support for the non-monophyly of Stoliczkia, as presently constituted, with S. borneensis being more closely related to Xenodermus than to the Northeast Indian S. vanhnuailianai. Based on phylogenetic relationships and morphological distinctiveness, we transfer Stoliczkia borneensis to a new monotypic genus endemic to Borneo, Paraxenodermus gen. nov. We also present new morphological data for P. borneensis.

Key words

Borneo, endemic, morphology, Paraxenodermus gen. nov., phylogeny, taxonomy

Introduction

The caenophidian snake family Xenodermidae Gray, 1849 includes five currently recognised genera, namely Achalinus Peters, 1869, Fimbrios Smith, 1921, Parafimbrios Teynié, David, Lottier, Le, Vidal & Nguyen, 2015, Xenodermus Reinhardt, 1836 and Stoliczkia Jerdon, 1870. Achalinus is the most speciose of these genera, with 19 currently recognised species, 10 of which were described in the past five years (Uetz et al. 2021). Achalinus spp. are distributed from north of 20° latitude in Vietnam, across south-east China and into central Japan (Fig. 1). Fimbrios comprises two species (Smith 1921; Ziegler et al. 2008), distributed in southern and central Laos and Vietnam, with a record from southern Cambodia (Fig. 1). The two species of the recently described Parafimbrios are thus far recorded only from northern Vietnam, Laos and Thailand (Fig. 1). The monotypic Xenodermus may be the most widespread xenodermid species, occurring in southernmost Myanmar, Thailand, peninsular Malaysia, Borneo, Sumatra and Java (Fig. 1). The genus Stoliczkia currently includes three poorly known species with a particularly disjunct distribution, two occurring in Northeast India (S. khasiensis Jerdon, 1870 and S. vanhnuailianai Lalronunga, Lalhmangaiha, Zosangliana, Lalhmingliani, Gower, Das & Deepak, 2021) and one in northern and western Borneo (S. borneensis) (Das 2021; Stuebing et al. 2014) (Fig. 1). Previously, molecular data were available only for S. borneensis (Vidal and Hedges 2002), and few morphological data for the <10 reported specimens of Stoliczkia (sensu lato) had been published (Lalronunga et al. 2021). In this paper, we report the first molecular data for Northeast Indian Stoliczkia and new morphological data for S. borneensis. We test the monophyly of Stoliczkia, and describe a new genus for the Bornean species.

Figure 1. 

Left panel: Multilocus ML phylogeny showing relationships of xenodermid snakes. Numbers at internal branches are: ML bootstrap support / BI posterior probability support. Right panel: map depicting distribution of all currently recognised xenodermid genera. Source: GBIF, Teynié et al. 2015, Ziegler et al. 2008). Additional localities for Xenodermus javanicus from Smith, 1943; Tweedie, 1954; Taylor, 1965; David and Vogel, 1996; Wallach et al. 2014).

Materials and Methods

DNA extraction and amplification

We collected a liver sample from the holotype (and only reported specimen of) Stoliczkia vanhnuailianai, preserved it in 99% ethanol and stored in –20°C freezer. We extracted genomic DNA using the DNeasy (Qiagen) blood and tissue kit and amplified partial sequences of four mitochondrial (mt) and two nuclear (nu) genes. The mt genes are 16S rRNA (16S, 528 base pairs [bp]), 12S rRNA (12S, 317 bp), cytochrome b (cytb, 654 bp) and cytochrome oxidase subunit 1 (co1, 710 bp); and the nu markers are oocyte maturation factor (cmos, 449 bp) and neurotrophin-3 (nt3, 507 bp) . PCR conditions followed previously reported protocols (16S, primers 16Sar-L and 16Sbr-H: Palumbi et al. 1991; 12S, primers 12Sa-L and 12Sb-H: Palumbi et al.1991; cytb, primers GluDG L: Palumbi 1996 and H16064: Burbrink et al. 2000; co1, primers LCO 1490 (F) and HCO 2198 (R): Folmer et al. 1994; cmos, primers S77 and S78: Lawson et al. 2005; nt3, primers nt3f and nt3r: Townsend et al. 2008). Sanger sequencing was carried out using the same primers. We assembled contigs from bidirectional sequence chromatograms and edited them in SnapGene Viewer (http://www.snapgene.com/products/snapgene_viewer).

Phylogeny

We aligned the new sequences for Stoliczkia vanhnuailianai with eight other xenodermids, and an outgroup, the non-xenodermid caenophidian Acrochordus granulatus. We checked for stop codons in unexpected regions by translating nucleotide alignments to amino acids for protein-coding genes (cytb, co1, cmos, nt3) using MEGA 7 (Kumar et al. 2016). We aligned sequences using ClustalW (Thompson et al.1994) in MEGA 7 (Kumar et al. 2016) with default settings (alignments online from the Natural History Museum data portal: https://doi.org/10.5519/gbzyjuli).

First, we built individual gene trees using Maximum Likelihood (ML). Based on availability of sequence data, we selected one species per xenodermid genus (though included both S. borneensis and S. vanhnuailianai for Stoliczkia) and the outgroup. We then aligned and concatenated the six gene sequences into a single dataset (3122 basepairs in length) with ten tips, including the outgroup (Table 1).

Table 1.

GenBank accession numbers and voucher numbers for the sequences used in this study. Sequences used in the ML and BI concatenated phylogeny are indicated with an asterisk. Accession codes for sequences newly generated in this study are in bold text.

Species Family 12S 16S cytb cmos nt3 co1
Acrochordus granulatus* Acrochordidae AF544738 AF544786 AF217841 HM234057 FJ434082 MH273113
Acrochordus javanicus Acrochordidae KX694587 AF512745 KX694897 HM234058 KX694991 LC533890
Agkistrodon contortrix Viperidae (Crotalinae) AF156587 AF156566 EU483383 MN135583
Ahaetulla pulverulenta Colubridae (Ahaetuliinae) KC347304 KC347339 KC347454 KC347378
Anilius scytale Aniliidae AF544753 FJ755180 U69738 AF544722 FJ434066
Anomochilus leonardi Cylindrophiidae + Anomochiliidae AY953430 AY953431
Aparallactus capensis Atractaspididae (Aparallactinae) FJ404129 AY188045 AY188006 AY187967
Aplopeltura boa Pareidae (Pareinae) AF544761 AF544787 JF827673 JF827696 FJ434085
Asthenodipsas laevis Pareidae (Pareinae) KX660197 KX660469 KX660336
Azemiops feae Viperidae (Azemiopinae) KX694579 AF057234 AY352747 AF544695 KX694977 KP403570
Bitis nasicornis Viperidae (Viperinae) DQ305411 AY188048 DQ305457 AY187970 MH273549
Boa constrictor Boidae AF512744 AB177354 AB177354 AF544676 MH140079
Boaedon fuliginosus Lamprophiidae (Lamprophiinae) FJ404169 AY188079 AF471060 FJ404270 FJ434094 AY122663
Bothrolycus ater Lamprophiidae (Lamprophiinae) FJ404144 AY611859 AY612041 FJ404347 MH273562
Buhoma depressiceps Lamprophiidae incertae sedis FJ404147 AY611860 AY612042 AY611951
Buhoma procterae Lamprophiidae incertae sedis FJ404148 AY611818 AY612001 AY611910
Bungarus fasciatus Elapidae EU547135 EU579523 EU579523 AY058924 KX694998 KY769767
Calabaria reinhardtii Calabariidae KF576842 Z46494 AY099985 AF544682 MH273568
Calamaria pavimentata Colubridae (Calamariinae) MH445959 KX694624 AF471081 AF471103 KX694999 MK064858
Candoia carinata Candoiidae AF544741 EU419850 AY099984 AY099961 FJ434077
Cantoria violacea Homalopsidae EF395873 KX694627 EF395897 KX695001
Casarea dussumieri Bolyeridae AF544754 AF544827 U69755 AF544731 FJ434069
Charina bottae Charinidae (Charininae) AF544743 AF544816 AY099986 AY099971 FJ434079
Chilabothrus striatus Boidae KC329933 KC329991 DQ465554
Contia tenuis Colubridae (Dipsadinae) AY577021 AY577030 GU112384 AF471134 KU986070
Corallus annulatus Boidae JX244286 KC750012 KC750007 MH140107
Cylindrophis ruffus Cylindrophiidae+Anomochilidae MK065683 AB179619 AB179619 AF471133 MK064906
Daboia russelii Viperidae (Viperinae) DQ305413 EU913478 EU913478 AF471156 GQ225661
Ditypophis vivax Lamprophiidae FJ404150 AY188052 AY188013 KU567322
Epicrates cenchria Boidae AF368059 HQ399501 KC330008 JX576186
Eryx colubrinus Erycidae AF544747 AF544819 U69811 AF544716 DQ465569
Eryx conicus Erycidae GQ225680 AF512743 GQ225658
Eunectes notaeus Boidae AF368057 AM236347 HQ399499 HQ399536
Gerrhopilus mirus Gerrhopilidae AM236345 AM236345 AM236345 GU902566 AM236345
Grayia ornata Colubridae (Grayiinae) AF158434 AY611866 AY612048 AF544684 KX695019 MH274058
Hologerrhum philippinum Lamprophiidae (Cyclocorinae) MG458758 MG458766
Homoroselaps lacteus Lamprophiidae (Atractaspidinae) KX694590 AY611809 AY611992 AY611901 KX695021
Liasis mackloti Pythonidae EF545024 EF545051 U69839 AF544726 FJ434075
Liopholidophis sexlineatus Lamprophiidae (Pseudoxyrhophiinae) FJ404174 AY188063 DQ979985 AY187985 JQ909421
Liotyphlops albirostris Anomalepididae AF366693 AF366762 AF544672 AF544727 MH140260
Loxocemus bicolor Loxocemidae AF512737 AF544828 AY099993 AY444035 FJ434072
Micrelaps bicoloratus Lamprophiidae (Aparallactinae) DQ486349 DQ486173
Mimophis mahfalensis Lamprophiidae (Psammophiinae) KX694543 AY188070 DQ486461 AY187992 KX695030 JQ909482
Naja (Afronaja) mossambica Elapidae GQ359658 AY611813 AY611996 AY611905
Naja (Boulengerina) melanoleuca Elapidae U96801 AY611812 AY611995 AY611904 MH274485
Oxyrhabdium leporinum Lamprophiidae (Cyclocorinae) AF471029 DQ112081
Oxyuranus scutellatus Elapidae EU547100 EU547149 EU547051 EU546916
Pareas carinatus Pareidae (Pareinae) AF544773 AF544802 JF827677 JF827702 FJ434086
Prosymna janii Lamprophiidae (Prosymninae) FJ404193 FJ404222 FJ404319 FJ404293
Pseudaspis cana Lamprophiidae (Pseudaspidinae) FJ404187 AY611898 AY612080 DQ486167
Pseudoxenodon karlschmidti Colubridae (Pseudoxenodontinae) KX694578 JF697330 AF471080 AF471102 KX695042 MK064781
Python bivittatus Pythonidae KF010492 KF010492 JX401131 AF435016 KF010492
Rhinophis drummondhayi Uropeltidae AY700997 AY701028 AF544673 AF544719 FJ434071
Sanzinia madagascariensis Sanziniidae EU403571 AY336066 U69866 EU403580 MH274606
Tropidophis feicki Tropidophiidae AF512733 AF512733 KF811124 KF811110
Ungaliophis continentalis Charinidae (Ungaliophiinae) AF512741 AF544833 U69870 AF544724 FJ434081
Xenopeltis unicolor Xenopeltidae AF512735 AB179620 AB179620 AF544689 FJ434073 MK064839
Xenophidion schaeferi Xenophidiidae AY574279 MK070320 MK070322
Xylophis perroteti Pareidae (Xylophiinae) MK340908 MN970042 MK344193
Achalinus rufescens* Xenodermidae KX694570 KX694613 KX694895 KX694990
Achalinus spinalis* Xenodermidae MK065581 MK194153 MK201476 MK064822
Achalinus zugorum* Xenodermidae MT503100 MT513238 MT502775
Fimbrios klossi* Xenodermidae KX694894 KP410745
Parafimbrios lao* Xenodermidae KP410746
Parafimbrios vietnamensis* Xenodermidae MH884515
Stoliczkiaborneensis* Xenodermidae AF544779 AF544808 AF544721 FJ434083
Stoliczkia vanhnuailianai* Xenodermidae OL352693 OL352694 OL422473 OL422475 OL422474 OL422476
Xenodermus javanicus* Xenodermidae AF544781 AF544810 AF544810 AF544711

We used PartitionFinder2 (Lanfear et al. 2017) to identify the best-fit partition scheme for the concatenated dataset and the best-fit model of sequence evolution for each partition as determined by the Bayesian Information Criterion (BIC), using the default greedy algorithm linked to branch lengths (Lanfear et al. 2012). The best-fit scheme for the concatenated dataset comprises six partitions, by gene and by codon position (Table 2). We performed Maximum Likelihood (ML; Felsenstein 1981) phylogenetic analyses with RAxML GUI Ver. 2.0 (Edler et al. 2021), using the GTRGAMMA model of sequence evolution, which is recommended over GTR+G+I because the 25 rate categories account for potentially invariant sites (Stamatakis 2006). For Bayesian (BI) phylogenetic analyses we used MrBayes 3.2.6 (Ronquist et al. 2012) via the XSEDE portal CIPRES Science Gateway v3.3 (Miller et al. 2010), with default prior settings and with all six partitions assigned their best-fit model as determined by PartitionFinder (Table 2). We set up two separate runs with four Markov chains each, initiated from random trees and allowed to run for one million generations, sampling every 100 generations and discarding the first 25% of trees as “burn-in”. We terminated the analyses when the standard deviation of split frequencies was less than 0.005, and then constructed majority rule consensus trees. We checked for effective sample size (ESS) values using Tracer 1.7 (Rambaut et al. 2014), all parameter values had ESS values >200. We quantified support for internal branches in ML and BI trees using bootstrap (500 replicates) and posterior probability, respectively. We assessed levels of support for relationships incompatible with optimal trees by inspecting bipartition tables of ML bootstrap or BI posterior probability trees using PAUP* 4.0a 169 (X86) (Swofford 2003). We rooted the trees with Acrochordus granulatus because it is a non-xenodermid caenophidian snake (Figueroa et al. 2016; Deepak et al. 2018; Zaher et al. 2019).

Table 2.

Partitions and models of sequence evolution used in the ML and BI phylogenetic analyses for the concatenated dataset. 1st, 2nd and 3rd refer to the codon position.

Partitions Sites BI ML
1 co1 1st, nt31st K80+I GTR+G
2 cytb 2nd, co12nd HKY+I GTR+G
3 cytb 3rd, co13rd HKY+G GTR+G
4 12S, 16S, cytb 1st GTR+G GTR+G
5 cmos 1st, cmos2nd, nt31st, nt32nd K80+I GTR+G
6 cmos 3rd HKY GTR+G

Molecular dating

We aligned a larger dataset with 68 tips including two scolecophidians (Gerrhopilus mirus and Liotyphlops albirostris) and representatives of all subfamilies of Alethinophidia, including nine xenodermids (sampling all five currently recognised genera). We aligned this dataset separately using the same methods outlined above (alignments available at: https://doi.org/10.5519/gbzyjuli). We applied seven fossil calibrations (Table 3), largely those recommended by Head (2015) and Head et al. (2016) as recently utilized by Deepak et al. (2021). Additionally, we set the root of the tree at a maximum age of 128 Ma and a minimum age of 123 Ma (i.e., Early Cretaceous, to correspond to the approximate age of the Serpentes root (based on point or mean values from Zheng and Wiens, 2016; Miralles et al. 2018; Burbrink et al. 2020). The best-fitting partition scheme and model(s) of sequence evolution identified using PartitionFinder had ten partitions (Appendix 1). Initially we carried out divergence dating by analysing this dataset and partition scheme with BEAST version 2.5 (Bouckaert et al. 2019) using XSEDE in the CIPRES Science Gateway v3.3 (Miller et al. 2010) under a Yule tree process. We assigned a relaxed log-normal clock for each partition of the concatenated BEAST analysis. We set up two independent runs, each employing the Markov Chain Monte Carlo (MCMC) for 100,000,000 generations, sampling every 5,000 trees. We obtained effective sample size (ESS) values using Tracer 1.7 (Rambaut et al. 2014). ESS values were below 100 for the priors and posteriors employing the best-fit model identified using PartitionFinder. We also repeated the analysis implementing the less-complex HKY model for the partitions but otherwise using the same settings. However, in this second analysis, we recovered ESS values above 200 for all the priors and posteriors for the two independent runs.

Table 3.

Parameter values for fossil calibrations used in the BEAST divergence dating analysis. Ages in Ma. All maximum ages soft, except hard maximum for calibration 6.

Calibration Node calibrations Offset Maximum age Mean Standard deviation
1 Oldest divergence within crown Alethinophidia 93.9 100.5 1.5 1.25
2 Oldest divergence between non-xenodermid colubroids and their closest living relative (Xenodermidae) 50.5 72.1 6.1 1.25
3 Divergence between Boinae and its sister taxon (Erycinae + Candoiinae) 58 64 1.8 1.25
4 Divergence between Corallus and (Chilabothrus + (Epicrates + Eunectes)) 50.2 64 4 1.25
5 Divergence between Viperinae and Crotalinae 20 23.8 1 1.25
6 Divergence between Acrochordus javanicus and (A. ararfurae + A. granulatus) 18.1 23.1 1.5 1.25
7 Oldest divergence between Naja (Afronaja) and Naja (Boulengerina) 17 20 1 1.25

Morphology

We provide here morphological and meristic data for two specimens of Stoliczkia borneensis (BMNH 1946.1.15.58 and UNIMAS 8002) and additional published information on unspecified specimens from Stuebing et al. (2014). Total length, snout-vent length and tail length were measured with thread and a ruler to the nearest 1 mm. Other dimensions were recorded with dial calipers, to the nearest 0.1 mm. Bilateral scale counts separated by a comma are reported in left, right order. Ventral scales were counted following Dowling (1951). Length and width of head scales were measured at the longest and the widest points of the respective scale(s). Eye diameter was measured horizontally.

Museum abbreviations

UNIMAS—Universiti Malaysia Sarawak; NHMUK—Natural History Museum, London (specimen numbers have a BMNH prefix); ZSIK—Zoological Survey of India, Kolkata, and ZRC—Herpetofauna and fish fauna collection at Lee Kong Chian Natural History Museum, Singapore.

Results

Phylogeny

The single-gene ML trees are shown in Fig. 2. Depending on taxon sampling (limited by availability of sequence data), generally S. borneensis and S. vanhnuailianai show close affinities with Xenodermus and with Achalinus, respectively. Although ML bootstrap support for many relationships are not strong (<90), support for Stoliczkia monophyly in the four gene trees for which both species were sampled is negligible, being only 25 for 16S and 0–0.2 for 12S, cmos and nt3. The ML and BI trees derived from the concatenated dataset agree in the set of relationships depicted (Fig. 1), with generally moderate (70–90 ML bootstrap; 0.80–0.90 BI posterior probability) to high support (>90 ML; >0.95 BI). Importantly, there is zero bootstrap or posterior probability support for Stoliczkia monophyly in these latter trees. Instead, the best-supported relationships that are incompatible with this optimal set of relationships for Stoliczkia spp. are for Xenodermus javanicus being more closely related to Fimbrios and Parafimbrios (ML bootstrap = 20; BI posterior probability = 0) and for S. borneensis being more closely related to Fimbrios and Parafimbrios (ML bootstrap = 5; BI posterior probability = 9). Thus, we conclude that the available DNA sequence data provide good to strong support for S. borneensis being more closely related to Xenodermus than to S. vanhnuailianai, and for S. vanhnuailianai being more closely related to Achalinus than to S. borneensis, and very strong support for non-monophyly of Stoliczkia.

Figure 2. 

Single-gene ML trees showing inferred phylogenetic relationships of xenodermid snakes, rooted with outgroup Acrochordus granulatus. ML bootstrap support is shown at internal branches. Scale bars indicate substitutions per site.

Morphology

Previously, extensive data were available for only a single vouchered specimen (the holotype, BMNH 1946.1.15.58) of Stoliczkia borneensis (Lalronunga et al. 2021). Data for an additional specimen (UNIMAS 8002) are presented in Table 4. This specimen agrees with data presented by Lalronunga et al. (2021) corroborating that S. vanhnuailianai resembles the type species of the genus, S. khasiensis much more closely than either does S. borneensis. Notable differences between the Bornean species and the two Northeast Indian species include presence of 4–6 small scales between the frontals and prefrontals in S. borneensis which are absent in the Northeast Indian species; supralabials not contacting the eye in S. borneensis versus contacting the eye S. vanhnuailianai and S. khasiensis; 10 or 11 supralabials versus 8 or 9 supralabials. Although S. borneensis is seemingly most closely related to Xenodermus (Fig. 2), the two taxa differ markedly in external morphology—for example, X. javanicus lacks large scales on the head other than at the snout tip whereas S. borneensis additionally has large parietal and frontal shields. Xenodermus javanicus and S. borneensis share a derived condition of having more small, irregular head scales than are present in other xenodermids.

Table 4.

Morphometric (in mm) and meristic data for Paraxenodermus borneensis. Data for the holotype (*) from Lalronunga et al. (2021). Data for unspecified specimens from Stuebing et al. (2014).

Voucher Number UNIMAS 8002 BMNH 1946.1.15.58* Unspecified specimens
Sex male male
Snout-vent length 481 541
Tail length (Ta) 232 248
Total length (TL) 713 789
TaL / TL 0.33 0.31
Horizontal eye diameter 2.7 2.8
Head length 9.6 17.9
Head width 8.0 10.8
Head height 5.2 5.5
Dorsal scale rows at one head
length behind head
31 31
Dorsal scale rows at midbody 31 32 31–35
Dorsal scale rows at one head length before vent 25 25
Ventrals 206 208 205–210 (“females only”)
Subcaudals 128 123 117–124
Anal shields 1 1
Supralabials 10,10 10,- 10 or 11
Supralabials touching eye 0 0
Infralabials 14,13 14,-
Infralabials touching anterior genials 1–2 1–3
Suboculars 3,3 3,3
Loreals 1,1 (+ 2 very small scales on both sides close to nasals) 1,1 (+ 2 very small scales on both sides close to nasals)
Preoculars 2,2 3,3
Supraoculars 3,3 2,2
Postoculars 4,4 2,4
Anterior temporals 0,0 0,0

Systematics

Stoliczkia — (Jerdon, 1870)

Content— S. khasiensis (Fig. 3A–B) and S. vanhnuailianai (Fig. 3C–D)

Stoliczkaia — Boulenger, 1890

Stolickaia — Palacky, 1898

Stolickaja — Palacky, 1898

Estoliczkaia — Briceño-Rossi, 1934

Stoliczkaia — Smith, 1943

Stolzickia — Taub, 1967

Stoliczkai — Murthy and Pillai in Majupuria, 1986

Diagnosis

This genus can be diagnosed based on the combination of the following features: (1) maxillary teeth small and subequal, (2) head very distinct from (much wider than) ‘neck’, with large shields on dorsal aspect, (3) posterior one-third of the head and posterior temporal region covered with small scales like those of the anterior end of the body, (4) 3 small scales between parietal and supralabial shields immediately behind eye (5) 8–9 supralabials, (6) nostril in a large concave nasal, (7) body slender and somewhat laterally compressed, (8) ventrals large, and (9) dark dorsum and pale venter meet along a regular straight line ventrolaterally and subcaudals partially or completely darker than venter.

Figure 3. 

Line drawings of Stoliczkia khasiensis (A, B), Stoliczkia vanhnuailianai (C, D) and Paraxenodermus borneensis (E, F) based on ZSIK 14945, BNHS 3656 and BMNH 1946.1.15.58 respectively. Genus characteristics are highlighted in different colours: 1) some supralabials in contact with eye in Stoliczkia, separated by circumorbital scales in Paraxenodermus; 2) fewer supra- and infralabials in Stoliczkia than in Paraxenodermus; 3) single prefrontal in Stoliczkia versus 2–3 in Paraxenodermus, 4) fewer scales between parietal and supralabials immediately behind eye in Stoliczkia than in Paraxenodermus, and 5) small row of scales between frontal and prefrontals absent in Stoliczkia, present in Paraxenodermus. Note small scales behind the temporals are indicative rather than precisely accurate. Pale grey coloured areas are bare skin exposed between scales. Illustrations by V. Deepak and Surya Narayanan. Scale bars = 10 mm.

Distribution

This genus is restricted to Northeast India (Fig. 1). Stoliczkia khasiensis is thus far known only from Khasi hills, Meghalaya state, India and the recently described Stoliczkia vanhnuailianai is known only from Mizoram state, India.

Etymology

The genus is named after the Moravian-born Ferdinand Stoliczka (1838–1874). A geologist-natural historian, he was appointed as a palaeontologist with the Geological Survey of India in 1863. Stoliczka collected vertebrates and molluscs from northern India, Andaman and Nicobar Islands, Myanmar and the Malay Peninsula. He served as the official Naturalist with the Second Mission to Yarkand, in central Asia. A biography and a list of published works and reports by Stoliczka can be found in Kolmaš (1982).

Paraxenodermus , gen. nov.

Type species

Paraxenodermus borneensis (Boulenger, 1899).

Type locality

Mount Kinabalu, North Borneo (4,200 ft / 1,280 m); the holotype is deposited in the Natural History Museum, London as BMNH 1946.1.15.58; collected by Richard Hanitsch in March, 1899.

Content—Paraxenodermus borneensis

Paraxenodermus borneensis

Figs 3E–F, 4 & 5

Stoliczkaia borneensis Boulenger 1899: 452

Stoliczkaia borneensisde Rooij 1917: 45

Stoliczkaia borneensis — de Haas 1950: 530

Stoliczkaia borneensisHaile 1958: 766

Stoliczkaia borneensisStuebing: 1991: 329

Stoliczkia borneensisManthey and Grossmann 1997: 394

Stoliczkia borneensisMalkmus et al. 2002

Stoliczkia borneensisDas 2006a: 9

Stoliczkia borneensisDas 2006b: 500–501

Stoliczkia borneensis — Das 2012 :153

Stoliczkia borneensis — Das 2018: 151, 169

Stoliczkia borneensisStuebing et al. 2014: 79

Stoliczkia borneensisWallach et al. 2014: 689

Stoliczkia borneensisBoundy 2020: 172

Stoliczkia borneensisLalronunga et al. 2021: 569–580

Diagnosis

This genus can be diagnosed based on the combination of the following features: (1) maxillary teeth small and subequal, (2) head very distinct from (much wider than) ‘neck’, with large shields on dorsal aspect, (3) posterior one-third of the head and posterior temporal region covered with small scales like those of the anterior of the body, (4) numerous small scales between parietal and supralabial shields immediately behind eye, (5) a row of 4–6 small scales between the frontal and prefrontal shields, (6) 10–11 supralabials, (7) nostril in a large concave nasal, (8) body slender and somewhat laterally compressed, (9) ventrals large, and (10) dorsum with numerous dorsolateral and middorsal pale blotches, venter pale with brown patches and subcaudals dark grey.

Figure 4. 

Holotype of Paraxenodermus borneensis (Boulenger, 1899), BMNH 1946.1.15.58. Photographs by Kevin Webb. Scale bar increments in mm.

Comparison to other xenodermid genera

Morphologically Paraxenodermus borneensis differs from all other xenodermid snakes by a combination of the following characters: presence of head shields (absent in Xenodermus javanicus, other than at snout tip), approximately one-third of the head covered with small scales similar to dorsal scales on the anterior of the body (versus head scales distinct from body scales in Achalinus, Fimbrios and Parafimbrios), head much wider than ‘neck’ (versus head indistinct from neck in Fimbrios, Parafimbrios and Achalinus) and presence of a row of small scales between frontal and prefrontal scales (absent in Stoliczkia).

Distribution

The new genus is restricted to the island of Borneo and so far, reported from the Kinabalu Massif (Boulenger 1899) and the contiguous Crocker Range, both in Sabah, in the northeastern part of Borneo (Das 2006a), as well as in the isolated Gunung Murud (Das 2006b), in Sarawak State. https://www.inaturalist.org/observations?taxon_id=28573). Information is not available for the holotype, but all other reported individuals were found late at night, moving slowly on rocky banks of streams at elevations of 950–2,100 m above sea level (Das 2006a).

Variation

The two examined specimens of Paraxenodermus borneensis, the holotype BMNH 1946.1.15.58 and UNIMAS 8002, differ slightly in the number of small scales lying between the frontal and prefrontals, being six and four, respectively. We counted six small scales in this position in images of a live individual on the internet (https://www.inaturalist.org/taxa/28573). UNIMAS 8002 also differs from BMNH 1946.1.15.58 in having a two more ventrals (208 versus 206) and five additional subcaudals (128 versus 123), and in being smaller (713 mm versus 789 mm total length).

Etymology

The generic name Paraxenodermus is composed of the modern Latin generic name Xenodermus and the Latin adjective par (paris), meaning, among other possibilities, “similar to”.

Figure 5. 

Paraxenodermus borneensis in life (ZRC 2.5731), from Crocker Range, Sabah, in the north-western Borneo. Sequences for this specimen was published in Vidal and Hedges (2002) and used in this study. Photograph by Indraneil Das.

Discussion

Taken at face value, our phylogenetic results and the distribution of xenodermid genera (Fig. 1) indicate that there are two main radiations within Xenodermidae; one in Northeast India, northern mainland Southeast Asia and Japan (Stoliczkia + Achalinus sensu stricto) and one in eastern mainland Indochina and southeast Sundaland (Fimbrios, Parafimbrios, Paraxenodermus, Xenodermus). The most parsimonious interpretation is that the most recent common ancestor of these two main xenodermid radiations occurred in mainland Indochina, suggested by our dating analyses to be approximately 66.7–44.6 Ma (Fig. 6). However, this would be better tested in future by undertaking probabilistic biogeographic analyses of a more broadly taxonomically sampled tree.

Establishment of a new genus for S. borneensis and a new understanding of phylogenetic relationships removes the exceptional geographic disjunction presented by the previous concept of Stoliczkia. These results also strengthen evidence for endemic radiations within both Borneo (e.g. Blackburn et al. 2010; Wood et al. 2012; Hertwig et al. 2013; Fritz et al. 2014) and Northeast India (e.g., Pawar et al. 2007; Kamei et al. 2012).

Figure 6. 

BEAST chronogram showing estimated divergence times for xenodermid snakes inferred from 68 tips for a concatenated mt and nu dataset. Numbers at internal branches indicate mean divergence ages, with blue bars showing 95% highest posterior density intervals. See Appendix 2 for complete dated phylogeny.

Acknowledgements

We thank K. Lalhmangaiha and Isaac Zosangliana for their support in the field. Specimen of S. vanhnuailianai was collected under the research and collection permission (A.38011/5/2011-CWLW/338) issued by the Department of Environment, Forest and Climate Change, Government of Mizoram. AD’s research is supported by SERB-DST (CRG/2018/000790) and Director, Wildlife Institute of India. Special thanks are due to Malsawmdawngliana for research assistance. Sabah field work by I. Das was supported by research grant UNIMAS 192/99(4), under research permit from Sabah Parks TS/PTD/5/5 Jld.14(76). UNIMAS 8002 from Sarawak was collected under research grant IRPA 08-02-09-10007-EA0001 by the Ministry of Science, Technology and Environment, Government of Malaysia, under research permit from the Sarawak Biodiversity Centre, SBC-RP-0070-ID. VD’s contribution was supported in part by a Humboldt Fellowship. VD thanks Uwe Fritz for his support. SN thanks Aravind N.A for his support at ATREE. Kevin Webb (NHMUK, London) is thanked for expert photography of the holotype of Stoliczkia borneensis. We thank Pratyush P. Mohapatra ZSI, Jabalpur for sharing photographs of the Stoliczkia khasiensis specimen stored in ZSI, Kolkata. We thank Lee Grismer, Lưu Quang Vinh and an anonymous reviewer for their comments and suggestions which improved this manuscript.

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Appendix 1

Partitions and models of sequence evolution used in the BEAST analyses for the 68 tips dataset. 1st, 2nd and 3rd refer to the codon position.

Partitions Sites model
1 12S GTR+G
2 16S, cytb 1st GTR+I+G
3 co1 1st, cytb2nd SYM+I+G
4 cytb 3rd GTR+I+G
5 co1 2nd HKY+G
6 co1 3rd GTR+I+G
7 cmos 1st, cmos2nd K80+G
8 cmos 3rd HKY+G
9 nt3 1st,nt32nd SYM+G
10 nt3 3rd HKY+G

Appendix 2

Specimens examined and/or photographed

Achalinus meridianus (holotype) BMNH 1946.1.12.31

Achalinus formosanus (holotype) BMNH 1946.1.7.78

Fimbrios klossi (syntype) BMNH 1946.1.15.87

Xenodermus javanicus (holotype) BMNH 1946.1.15.90

Stoliczkia khasiensis (holotype) BMNH 1946.1.15.67

Stoliczkia khasiensis ZSIK 14945

Stoliczkia borneensis (holotype) BMNH 1946.1.15.58

Stoliczkia borneensis UNIMAS 8002, ZRC 2.5731

Stoliczkia vanhnuailianai (holotype) BNHS 3656

Appendix 3

BEAST chronogram generated using concatenated-gene for representatives of all families and subfamilies of alethinophidian snakes. Error bars and the numbers at internal branches indicate 95% highest posterior densities for node ages.

Appendix 4

Paraxenodermus borneensis (UNIMAS 8002) from near Samling Camp at Ravenscourt, Lawas, Sarawak Malaysia. Photographs by Indraneil Das.